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The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.
Get your data
We are going to look at two mapping results- for samples C1_R1 and C2_R2. Download the corresponding bam files and index files from here onto your computer.
Some useful IGV Features
- SNPS
- Coverage tracks- to see coverage in one sample vs another acorss a certain location.
- All sorts of views for paired end data. These help us find analogous pair mappings, split mappings etc.
Launching IGV
| Warning |
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For the remainder of the tutorial, work on your local machine. NOT TACC! |
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